AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i262_3_5_1_28_bbur_reg_300.orf -o262_borburg_300.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -x5 -e 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.28
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RBB00553	213	3615
#2	RBB00769	20	3615
#3	RBB00550	22	3615
#4	RBB00549	89	3615

Motif number 1

AACTCTAATTCTTAAAATTAAACCTCCCAG	1	24	0	CTTAAAATTA	    0.952381	-190
TGAGATGTCGCAAAAAAATAACTCTAATTC	1	43	0	CAAAAAAATA	    0.934125	-171
TGCGACATCTCATAAAATTTAGGAATTTGA	1	61	1	CATAAAATTT	    0.964418	-153
GCTATCATTGACTAAAAATATTCAAATTCC	1	82	0	ACTAAAAATA	    0.978579	-132
AGAGGTTAAGAATAAAAATTCCGCCTTGAA	1	124	1	AATAAAAATT	    0.944073	-90
AATAGCGCTAAATAAAAATGTTCTTATGTT	1	155	1	AATAAAAATG	    0.883777	-59
 AATAATAATCCTTAAAATAAATTAAACTC	1	195	0	CCTTAAAATA	    0.921194	-19
  ATCTATCTCCTAAAATTATT        	2	3	0	CCTAAAATTA	    0.986544	-18
      TATTCCTAGAATTTACTTTTTAGT	4	5	1	CCTAGAATTT	    0.881244	-85
TTATACATTCACTAAAAAGTAAATTCTAGG	4	15	0	ACTAAAAAGT	    0.822185	-75
GTGAATGTATAATAAAATTAATTATTAATG	4	33	1	AATAAAATTA	    0.954149	-57
          CTAAAAAATATATACTCCTA	4	80	0	CTAAAAAATA	    0.860508	-10
          **********

Masking position 6
Map Score:   17.6824

Number of sites scoring better than the average of aligned sites = 1145
Number in coding regions = 759
Number in noncoding regions = 386
Number of orfs with sites within 600 bp upstream = 96
Fraction of orfs with sites within 600 bp upstream = 0.0154192


Motif number 2

AGGTTTAATTTTAAGAATTAGAGTTATTTT	1	29	1	TTAAGAATTA	    0.988046	-185
CTCATAAAATTTAGGAATTTGAATATTTTT	1	69	1	TTAGGAATTT	    0.982426	-145
AATTCAGAGGTTAAGAATAAAAATTCCGCC	1	119	1	TTAAGAATAA	    0.962649	-95
TGTTGGCTTTTTGGGAGTTTAATTTATTTT	1	181	1	TTGGGAGTTT	    0.915067	-33
TTAATTTATTTTAAGGATTATTATT     	1	199	1	TTAAGGATTA	    0.950836	-15
   AATAATTTTAGGAGATAGAT       	2	8	1	TTAGGAGATA	    0.932694	-13
ATAATTAACATTAATAATTAATTTTATTAT	4	41	0	TTAATAATTA	    0.941735	-49
CCTAAATCAATTAATAATTAACATTAATAA	4	54	0	TTAATAATTA	    0.941735	-36
ATTAATTGATTTAGGAGTATATATTTTTTA	4	69	1	TTAGGAGTAT	    0.935765	-21
          **********

Masking position 2
Map Score:   14.1656

Number of sites scoring better than the average of aligned sites = 369
Number in coding regions = 238
Number in noncoding regions = 131
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 3

       AAAATCAAAGCTCCTGGGAGGTTTA	1	4	1	ATCAACTCCT	    0.984708	-210
AATTCTTAAAATTAAACCTCCCAGGAGCTTTG	1	16	0	ATTAACTCCC	    0.991633	-198
GACTAAAAATATTCAAATTCCTAAATTTTATG	1	71	0	ATTAATTCCT	    0.979715	-143
GAGGTTAAGAATAAAAATTCCGCCTTGAAAAA	1	125	1	ATAAATTCCG	    0.921023	-89
CCTTAAAATAAATTAAACTCCCAAAAAGCCAA	1	183	0	AATAACTCCC	    0.980973	-31
          AATAATAATCCTTAAAATAAAT	1	202	0	AATATATCCT	    0.838291	-12
   CTAAAAAATATATACTCCTAAATCAATTA	4	71	0	ATAATCTCCT	    0.970871	-19
          *** ** *****

Masking position 5
Map Score:   6.39455

Number of sites scoring better than the average of aligned sites = 145
Number in coding regions = 96
Number in noncoding regions = 49
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 4

          **********

No masking
Map Score:   -5.58897e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 5

          **********

No masking
Map Score:   -5.58897e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 6

          **********

No masking
Map Score:   -5.58897e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0